Research workbench
Crystal structure of SARS-cov-2 main protease (mpro) Q192T mutant in complex with inhibitor GC376
Analyse Crystal structure of SARS-cov-2 main protease (mpro) Q192T mutant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DGB
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase NSP5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- B1S
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 304 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- B1S · (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.77 | 0.79 | 85 | empty |
| 2 | 562 | 0.62 | 0.74 | 72 | empty |
| 3 | 211 | 0.56 | 0.79 | 29 | B1S |
| 4 | 181 | 0.52 | 0.78 | 30 | B1S |
Interfaces
1 interface between chains.
- A–B · 1608 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 8DGB · Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Q192T Mutant in Complex with… · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 8DGB · PDBe 8DGB · UniProt P0DTD1
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